High-throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID)

BMC Bioinformatics

Volumn 6, Issue , 2005, Pages

  Zeeberg, Barry R ^a   Qin, Haiying ^b   Narasimhan, Sudarshan ^c   Sunshine, Margot ^c   Cao, Hong ^c   Kane, David W ^c   Reimers, Mark ^c   Stephens, Robert M ^d   Bryant, David ^d   Burt, Stanley K ^d   Elnekave, Eldad ^e   Hari, Danielle M ^e   Wynn, Thomas A ^e   Cunningham Rundles, Charlotte ^f   Stewart, Donn M ^b   Nelson, David ^b   Weinstein, John N ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

^c GENERAL DYNAMICS   (United States)

^d SAIC FREDERICK INC   (United States)

^e NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES   (United States)

^f MOUNT SINAI MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL INTERPRETATION; COMPUTATIONAL RESOURCES; EXPERIMENTAL PLATFORM; FALSE DISCOVERY RATE; GENE EXPRESSION PATTERNS; MICROARRAY EXPERIMENTS; MULTIPLE COMPARISON; TRANSCRIPTION FACTOR BINDING SITES;

BATCH DATA PROCESSING; GENE EXPRESSION; GRAPHICAL USER INTERFACES; MICROARRAYS; TOOLS; VISUALIZATION;

EXPERIMENTS;

CHEMICAL AGENT; GENOMIC DNA; TRANSCRIPTION FACTOR;

ARTICLE; AUTOANALYSIS; BINDING SITE; COMMON VARIABLE IMMUNODEFICIENCY; COMPUTER PROGRAM; CONTROLLED STUDY; DNA MICROARRAY; GENE EXPRESSION; HIGH THROUGHPUT SCREENING; HUMAN; IMAGE DISPLAY; KNOCKOUT GENE; MATHEMATICAL COMPUTING; CHROMOSOME MAP; CLUSTER ANALYSIS; COMPUTER INTERFACE; DEVICES; GENE EXPRESSION PROFILING; GENETIC DATABASE; GENETICS; INFORMATION PROCESSING; METABOLISM; PHENOTYPE; PROTEIN MICROARRAY; SCHISTOSOMIASIS;

AUTOMATIC DATA PROCESSING; BINDING SITES; CHROMOSOME MAPPING; CLUSTER ANALYSIS; COMMON VARIABLE IMMUNODEFICIENCY; DATA DISPLAY; DATABASES, GENETIC; GENE EXPRESSION PROFILING; HUMANS; PHENOTYPE; PROTEIN ARRAY ANALYSIS; SCHISTOSOMIASIS; SOFTWARE; SOFTWARE DESIGN; TRANSCRIPTION FACTORS; USER-COMPUTER INTERFACE;

EID: 23044478689     PISSN: 14712105     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-6-168     Document Type: Article

References (51)

1. Zeeberg BR, Feng W, Wang G, Wang MD, Fojo AT, Sunshine M, Narasimhan S, Kane DW, Reinhold WC, Lababidi S, et al.: GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol 2003, 4:R28.
2. GoMiner [http://discover.nci.nih.gov/gominer]
3. High-Throughput GoMiner [http://discover.nci.nih.gov/gominer/htgm.jsp]
4. Bonferroni [http://home.clara.net/sisa/bonhlp.htm]
5. Weinstein J, Myers T, O'Connor P, Friend S, Fornace A Jr, Kohn K, Fojo T, Bates S, Rubinstein, Anderson N, Buolamwini J, van Osdol W, Monks A, Scudiero D, Sausville E, Zaharevitz D, Bunow B, Viswanadhan V, Johnson G, Wittes, Paull K: An information-intensive approach to the molecular pharmacology of cancer. Science 1997, 275:343-349.
6. CIMminer [http://discover.nci.nih.gov/nature2000/tools/cimmaker.jsp]
7. GPL License [http://www.opensource.org/licenses/gpl-license.php]
8. GNU Project [http://www.gnu.org/]
9. Storey JD, Tibshirani R: Statistical significance for genome-wide studies. Proc Natl Acad Sci 2003, 100:9440-9445.
10. Spickett GP: Current perspectives on common variable immunodeficiency (CVID). Clin Exp Allergy 2001, 31:536-542.
11. Ballow M: Primary immunodeficiency disorders: antibody deficiency. J Allergy Clin Immunol 2002, 109:581-591.
12. Simonte SJ, Cunningham-Rundles C: Update on primary immunodeficiency: defects of lymphocytes. Clin Immunol 2003, 109:109-118.
13. Cunningham-Rundles C: Hematologic complications of primary immune deficiencies. Blood Rev 2002, 16:61-64.
14. Warnatz K, Wehr C, Drager R, Schmidt S, Eibel H, Schlesier M, Peter HH: Expansion of CD19(hi)CD21(lo/neg) B cells in common variable immunodeficiency (CVID) patients with autoimmune cytopenia. Immunobiology 2002, 206:502-513.
15. Cunningham-Rundles C, Siegal FP, Cunningham-Rundles S, Lieberman P: Incidence of cancer in 98 patients with common varied immunodeficiency. J Clin Immunol 1987, 7:294-299.
16. Mellemkjaer L, Hammarstrom L, Andersen V, Yuen J, Heilmann C, Barington T, Bjorkander J, Olsen JH: Cancer risk among patients with IgA deficiency or common variable immunodeficiency and their relatives: a combined Danish and Swedish study. Clin Exp Immunol 2002, 130:495-500.
17. Cunningham-Rundles C, Cooper DL, Duffy TP, Strauchen J: Lymphomas of mucosal-associated lymphoid tissue in common variable immunodeficiency. Am J Hematol 2002, 69:171-178.
18. Groth C, Drager R, Warnatz K, Wolff-Vorbeck G, Schmidt S, Eibel H, Schlesier M, Peter HH: Impaired up-regulation of CD70 and CD86 in naive (CD27-) B cells from patients with common variable immunodeficiency (CVID). Clin Exp Immunol 2002, 129:133-139.
19. McQuaid A, Tormey VJ, Trafford B, Webster AD, Bofill M: Evidence for increased expression of regulatory cytokine receptors interleukin-12R and interleukin-18R in common variable immunodeficiency. Clin Exp Immunol 2003, 134:321-327.
20. Di Renzo M, Serrano D, Zhou Z, George I, Becker K, Cunningham-Rundles C: Enhanced T cell apoptosis in common variable immunodeficiency: negative role of the fas/fasligand system and of the Bcl-2 family proteins and possible role of TNF-RS. Clin Exp Immunol 2001, 125:117-122.
21. Holm AM, Aukrust P, Aandahl EM, Muller F, Tasken K, Froland SS: Impaired secretion of IL-10 by T cells from patients with common variable immunodeficiency - involvement of protein kinase A type I. J Immunol 2003, 170:5772-5777.
22. Farrington M, Grosmaire LS, Nonoyama S, Fischer SH, Hollenbaugh D, Ledbetter JA, Noelle RJ, Aruffo A, Ochs HD: CD40 ligand expression is defective in a subset of patients with common variable immunodeficiency. Proc Natl Acad Sci U S A 1994, 91:1099-1103.
23. Schiffer R, Baron J, Dagtekin G, Jahnen-Dechent W, Zwadlo-Klarwasser G: Differential regulation of the expression of transporters associated with antigen processing, TAP1 and TAP2, by cytokines and lipopolysaccharide in primary human macrophages. Inflamm Res 2002, 51:403-408.
24. Faigle W, Raposo G, Tenza D, Pinet V, Vogt AB, Kropshofer H, Fischer A, de Saint-Basile G, Amigorena S: Deficient peptide loading and MHC class II endosomal sorting in a human genetic immunodeficiency disease: the Chediak-Higashi syndrome. J Cell Biol 1998, 141:1121-1134.
25. Abdulkadir SA, Ono SJ: How are class II MHC genes turned on and off? FASEB J 1995, 9:1429-1435.
26. Stead A, Douglas JG, Broadfoot CJ, Kaminski ER, Herriot R: Humoral immunity and bronchiectasis. Clin Exp Immunol 2002, 130:325-330.
27. Conley ME: Genetics of primary immunodeficiency diseases. Rev Immunogenet 2000, 2:231-242.
28. Wienands J: Signal transduction elements of the B cell antigen receptor and their role in immunodeficiencies. Immunobiology 2000, 202:120-133.
29. Notarangelo LD, Giliani S, Mella P, Schumacher RF, Mazza C, Savoldi G, Rodriguez-Perez C, Badolato R, Mazzolari E, Porta F, Candotti F, Ugazio AG: Combined immunodeficiencies due to defects in signal transduction: defects of the gammac-JAK3 signaling pathway as a model. Immunobiology 2000, 202:106-119.
30. Stagg AJ, Funauchi M, Knight SC, Webster AD, Farrant J: Failure in antigen responses by T cells from patients with common variable immunodeficiency (CVID). Clin Exp Immunol 1994, 96:48-53.
31. Sneller MC: Common variable immunodeficiency. Am J Med Sci 2001, 321:42-48.
32. NCBI Entrez [http://www.ncbi.nlm.nih.gov/Entrez/index.html]
33. Ji W, Naguib RN, Ghoneim MA: Neural network-based assessment of prognostic markers and outcome prediction in bilharziasis-associated bladder cancer. IEEE Transactions on Information Technology in Biomedicine 2003, 7:218-24.
34. Zacharia B, Sherman P: Atopy, helminths, and cancer. Medical Hypotheses 2003, 60:1-5.
35. Fadl-Elmula I, Kytola S, Leithy ME, Abdel-Hameed M, Mandahl N, Elagib A, Ibrahim M, Larsson C, Heim S: Chromosomal aberrations in benign and malignant bilharzia-associated bladder lesions analyzed by comparative genomic hybridization. BMC Cancer 2002, 2:5.
36. Samandouras G, King A, Kellerman AJ: Schistosoma haematobium presenting as an intrinsic conus tumour. British Journal of Neurosurgery 2002, 16:296-300.
37. Lucey DR, Maguire JH: Schistosomiasis. Infect Dis Clin North Am 1993, 7:635-653.
38. Elliott DE: Schistosomiasis. Pathophysiology, diagnosis, and treatment. Gastroenterol Clin North Am 1996, 25:599-625.
39. Hoffmann KF, Wynn TA, Dunne DW: Cytokine-mediated host responses during schistosome infections; walking the fine line between immunological control and immunopathology. Adv Parasitol 2002, 52:265-307.
40. Pearce EJ, MacDonald AS: The immunobiology of schistosomiasis. Nat Rev Immunol 2002, 2:499-511.
41. Hosack DA, Dennis G, Sherman BT, Lane HC, Lempicki RA: Identifying biological themes within lists of genes with EASE. Genome Biol 2003, 4:R70.
42. Al-Shahrour F, Díaz-Uriarte R, Dopazo J: FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics 2004, 20:578-580.
43. Robinson MD, Grigull J, Mohammad N, Hughes TR: FunSpec: a web-based cluster interpreter for yeast. BMC Bioinformatics 2002, 3:35.
44. Zhong S, Storch KF, Lipan O, Kao MC, Weitz CJ, Wong WH: GoSurfer: A graphical interactive tool for comparative analysis of large gene sets in gene ontology. Appl Bioinformatics 2004, 3:261-264.
45. GoSurfer [http://biosun1.harvard.edu/complab/gosurfer/]
46. Boyle EI, Weng S, Gollub J, Jin H, Botstein D, Cherry JM, Sherlock G: GO::TermFinder - open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics 2004, 20:3710-3715.
47. GO::TermFinder [http://search.cpan.org/dist/GO-TermFinder/]
48. Khatri P, Draghici S, Ostermeier GC, Krawetz SA: Profiling gene expression using onto-express. Genomics 2002, 79:266-270.
49. Ontology Traverser http://franklin.imgen.bcm.tmc.edu/rho/services/ index.jsp?page=OntologyTraverser
50. GO::TermFinder batch processing [http://search.cpan.org/dist/GO-TermFinder/examples/analyze.pl]
51. GO::TermFinder README [http://search.cpan.org/src/SHERLOCK/GO-TermFinder-0.7/README]